Round-up Feb 19th-Feb 25th

Illumina have sued Oxford Nanopore Technologies for patent infringement. This is based on Illumina holding two patents for the use of the MspA pore. ONT have historically used a different pore, but they have perhaps switched to MspA. GenomeWeb report Oxford Nanopore’s CEO Gordon Sanghera saying, “It is gratifying to have the commercial relevance of Oxford Nanopore products so publicly acknowledged by the market monopolist for NGS.”. All this in the context of ONT soon to have their IPO, and old industry hands pointing out that Illumina launched a patent suit against Complete Genomics just before their IPO. https://www.genomeweb.com/sequencing-technology/update-illumina-sues-oxford-nanopore-patent-infringement. Additional commentary on the unfolding drama: http://www.opiniomics.org/shots-fired-nanopore-wars-part-ii/.

For NGS data, methods that aggregate variation over genes in order to pick up on associations from case-control studies (e.g. VAAST) are all the rage. These are supplanting the variant-by-variant analyses that dominated the SNP chip world. Burden tests can be followed by procedures to identify actual causal variants (e.g. remove a variant if excluding this variant can lead to a smaller P-value for the gene). Another approach is to continue to score each variant separately, but test for association using “adaptive combination of P-values (ADA)” to pinpoint causal variants: http://www.nature.com/articles/srep21824